Temporal regulation of gene expression through integration of dynamics and modifications

The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. Here, we show that p53's post-translational modification state is altered between its first and second pulses of expression. We show that acetylations at two sites, K373 and K382, reduced in the second pulse and these acetylations differentially affected p53 target genes, resulting in changes in gene expression programs over time. This interplay between dynamics and modification may offer a strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells. To assess the effect of the temporal changes in p53 acetylation on gene expression systematically, we performed time-series RNA-Sequencing at hourly intervals for 9 hours following 10Gy X-ray irradiation in cells expressing either WT or 2KR p53 along with endogenous p53. Response were compared to untreated cells (0h after treatment). We used MCF7 breast carcinoma cell lines and performed the experiment in duplicates.